Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Escherichia coli Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic Escherichia coli (APEC) Classification

The Clermont scheme has been used for subtyping of Escherichia coli since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal E. coli and pathogenic E. coli, such as extraintestinal pathogenic E. coli (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal E. coli using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 E. coli from human hosts and poultry, including 84 human neonatal meningitis E. coli isolates, 88 human vaginal E. coli, 696 human uropathogenic E. coli, 197 healthy human fecal E. coli, 452 avian pathogenic E. coli (APEC), 200 retail poultry E. coli, 80 crop and gizzard E. coli from healthy poultry at slaughter and 199 fecal E. coli from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates’ strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.This article is published as Logue, Catherine M., Yvonne Wannemuehler, Bryon A. Nicholson, Curt Doetkott, Nicolle L. Barbieri, and Lisa K. Nolan. "Comparative analysis of phylogenetic assignment of human and avian ExPEC and fecal commensal Escherichia coli using the (previous and revised) Clermont phylogenetic typing methods and its impact on avian pathogenic Escherichia coli (APEC) classification." Frontiers in Microbiology 8 (2017): 283. DOI: 10.3389/fmicb.2017.00283. Copyright 2017 Logue, Wannemuehler, Nicholson, Doetkott, Barbieri and Nolan. Attribution 4.0 International (CC BY 4.0). Posted with permission

Comparison of Multilocus Sequence Analysis and Virulence Genotyping of Escherichia coli from Live Birds, Retail Poultry Meat, and Human Extraintestinal Infection

the Veterinary Preventive Medicine, Epidemiology, and Public Health Commons The complete bibliographic information for this item can be found a

Recombinant Iss as a Potential Vaccine for Avian Colibacillosis

Avian pathogenic Escherichia coli (APEC) cause colibacillosis, a disease which is responsible for significant losses in poultry. Control of colibacillosis is problematic due to the restricted availability of relevant antimicrobial agents and to the frequent failure of vaccines to protect against the diverse range of APEC serogroups causing disease in birds. Previously, we reported that the increased serum survival gene (iss) is strongly associated with APEC strains, but not with fecal commensal E. coli in birds, making iss and the outer membrane protein it encodes (Iss) candidate targets for colibacillosis control procedures. Preliminary studies in birds showed that their immunization with Iss fusion proteins protected against challenge with two of the more-commonly occurring APEC serogroups (O2 and O78). Here, the potential of an Iss-based vaccine was further examined by assessing its effectiveness against an additional and widely occurring APEC serogroup (O1) and its ability to evoke both a serum and mucosal antibody response in immunized birds. In addition, tissues of selected birds were subjected to histopathologic examination in an effort to better characterize the protective response afforded by immunization with this vaccine. Iss fusion proteins were administered intramuscularly to four groups of 2-wk-old broiler chickens. At 2 wk postimmunization, chickens were challenged with APEC strains of the O1, O2, or O78 serogroups. One week after challenge, chickens were euthanatized, necropsied, any lesions consistent with colibacillosis were scored, and tissues from these birds were taken aseptically. Sera were collected pre-immunization, postimmunization, and post-challenge, and antibody titers to Iss were determined by enzyme-linked immunosorbent assay (ELISA). Also, air sac washings were collected to determine the mucosal antibody response to Iss by ELISA. During the observation period following challenge, 3/12 nonimmunized chickens, 1/12 chickens immunized with 10 µg of GST-Iss, and 1/12 chickens immunized with 50 µg of GST-Iss died when challenged with the O78 strain. No other deaths occurred. Immunized chickens produced a serum and mucosal antibody response to Iss and had significantly lower lesion scores than nonimmunized chickens following challenge, regardless of the challenge strain. This study expands on our previous report of the value of Iss as an immunoprotective antigen and demonstrates that immunization with Iss can provide significant protection of chickens against challenge with three different E. coli strains.This article is from Avian Diseases 56, no. 1 (2012): 192–199, doi:10.1637/9861-072111-Reg.1.</p

Complete genome sequence of the avian-pathogenic Escherichia coli strain APEC O18

Avian-pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, a disease that affects all facets of poultry production worldwide, resulting in multimillion dollar losses annually. Here, we report the genome sequence of an APEC O18 sequence type 95 (ST95) strain associated with disease in a chicken.This article is published as Nicholson, Bryon A., Yvonne M. Wannemuehler, Catherine M. Logue, Ganwu Li, and Lisa K. Nolan. "Complete genome sequence of the avian-pathogenic Escherichia coli strain APEC O18." Genome Announcements 4, no. 6 (2016): e01213-16. DOI: 10.1128/genomeA.01213-16. Copyright 2016 Nicholson et al. Attribution 4.0 International (CC BY 4.0). Posted with permission

Complete Genome Sequence of the Neonatal Meningitis-Causing Escherichia coli Strain NMEC O18

Neonatal meningitis Escherichia coli (NMEC) is a common agent of neonatal bacterial meningitis, causing high neonatal mortality and neurologic sequelae in its victims. Here, we present the complete genome sequence of NMEC O18 (also known as NMEC 58), a highly virulent (O18ac:K1, ST416) strain.This article is published as Nicholson, Bryon A., Yvonne M. Wannemuehler, Catherine M. Logue, Ganwu Li, and Lisa K. Nolan. "Complete genome sequence of the neonatal meningitis-causing Escherichia coli strain NMEC O18." Genome Announcements 4, no. 6 (2016): e01239-16. DOI: 10.1128/genomeA.01239-16. Copyright 2016 Nicholson et al. Attribution 4.0 International (CC BY 4.0). Posted with permission

\u3ci\u3eEscherichia coli, Salmonella\u3c/i\u3e, and \u3ci\u3eMycobacterium avium\u3c/i\u3e subsp. \u3ci\u3eparatuberculosis\u3c/i\u3e in Wild European Starlings at a Kansas Cattle Feedlot

The prevalence of Escherichia coli, Salmonella spp., and Mycobacterium avium subsp. paratuberculosis isolated from the feces of wild European starlings (Sturnus vulgaris) humanely trapped at a feedlot in central Kansas was assessed. All E. coli and Salmonella isolates recovered were tested for antimicrobial susceptibility using National Antimicrobial Resistance Monitoring System panels and the E. coli isolates were classified as to their content of genes associated with pathogenic E. coli of birds and cattle, including cvaC, iroN2, ompTp, hlyF2, eitC, iss, iutA, ireA, papC, stxI, stxII, sta, K99, F41, and eae. Escherichia coli O157:H7 and Mycobacterium avium subsp. paratuberculosis were not detected and Salmonella was isolated from only three samples, two of which displayed antimicrobial resistance. Approximately half of the E. coli isolates were resistant to antimicrobial agents with 96% showing resistance to tetracycline. Only one isolate was positive for a single gene associated with bovine pathogenic E. coli. An interesting finding of this study was that 5% of the E. coli isolates tested met the criteria established for identification as avian pathogenic E. coli (APEC). Thus these findings suggest that starlings are not a significant source of Salmonella spp., Mycobacterium avium subsp. paratuberculosis, E. coli O157, or other shiga toxin–producing E. coli in this feedlot. However, they may have the potential to spread APEC, an important pathogen of poultry and a potential pathogen to human beings

Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Escherichia coli Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic Escherichia coli (APEC) Classification

The Clermont scheme has been used for subtyping of Escherichia coli since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal E. coli and pathogenic E. coli, such as extraintestinal pathogenic E. coli (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal E. coli using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 E. coli from human hosts and poultry, including 84 human neonatal meningitis E. coli isolates, 88 human vaginal E. coli, 696 human uropathogenic E. coli, 197 healthy human fecal E. coli, 452 avian pathogenic E. coli (APEC), 200 retail poultry E. coli, 80 crop and gizzard E. coli from healthy poultry at slaughter and 199 fecal E. coli from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates’ strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.This article is published as Logue, Catherine M., Yvonne Wannemuehler, Bryon A. Nicholson, Curt Doetkott, Nicolle L. Barbieri, and Lisa K. Nolan. "Comparative analysis of phylogenetic assignment of human and avian ExPEC and fecal commensal Escherichia coli using the (previous and revised) Clermont phylogenetic typing methods and its impact on avian pathogenic Escherichia coli (APEC) classification." Frontiers in Microbiology 8 (2017): 283. DOI: 10.3389/fmicb.2017.00283. Copyright 2017 Logue, Wannemuehler, Nicholson, Doetkott, Barbieri and Nolan. Attribution 4.0 International (CC BY 4.0). Posted with permission

The Impact of Media, Phylogenetic Classification, and E. coli Pathotypes on Biofilm Formation in Extraintestinal and Commensal E. coli From Humans and Animals

Extraintestinal pathogenic Escherichia coli (ExPEC) include avian pathogenic E. coli (APEC), neonatal meningitis E. coli (NMEC), and uropathogenic E. coli (UPEC) and are responsible for significant animal and human morbidity and mortality. This study sought to investigate if biofilm formation by ExPEC likely contributes to these losses since biofilms are associated with recurrent urinary tract infections, antibiotic resistance, and bacterial exchange of genetic material. Therefore, the goal of this study was to examine differences in biofilm formation among a collection of ExPEC and to ascertain if there is a relationship between their ability to produce biofilms and their assignment to phylogenetic groups in three media types – M63, diluted TSB, and BHI. Our results suggest that ExPEC produce relatively different levels of biofilm formation in the media tested as APEC (70.4%, p = 0.0064) and NMEC (84.4%, p = 0.0093) isolates were poor biofilm formers in minimal medium M63 while UPEC isolates produced significantly higher ODs under nutrient-limited conditions with 25% of strains producing strong biofilms in diluted TSB (p = 0.0204). Additionally, E. coli phylogenetic assignment using Clermont’s original and revised typing scheme demonstrated significant differences among the phylogenetic groups in the different media. When the original phylogenetic group isolates previously typed as group D were phylogenetically typed under the revised scheme and examined, they showed substantial variation in their ability to form biofilms, which may explain the significant values of revised phylogenetic groups E and F in M63 (p = 0.0291, p = 0.0024). Our data indicates that biofilm formation is correlated with phylogenetic classification and subpathotype or commensal grouping of E. coli strains.This article is published as Nielsen, Daniel W., James S. Klimavicz, Tia Cavender, Yvonne Wannemuehler, Nicolle L. Barbieri, Lisa K. Nolan, and Catherine M. Logue. "The impact of media, phylogenetic classification, and E. coli pathotypes on biofilm formation in extraintestinal and commensal E. coli from humans and animals." Frontiers in Microbiology 9 (2018): 902. DOI: 10.3389/fmicb.2018.00902. Copyright 2018 Nielsen, Klimavicz, Cavender, Wannemuehler, Barbieri, Nolan, and Logue. Attribution 4.0 International (CC BY 4.0). Posted with permission

mcr-1 identified in Avian Pathogenic Escherichia coli (APEC)

Antimicrobial resistance associated with colistin has emerged as a significant concern worldwide threatening the use of one of the most important antimicrobials for treating human disease. Here, we examined a collection (n = 980) of Avian Pathogenic Escherichia coli (APEC) isolated from poultry with colibacillosis from the US and internationally for the presence of mcr-1 and mcr-2, genes known to encode colistin resistance. Included in the analysis was an additional set of avian fecal E. coli (AFEC) (n = 220) isolates from healthy birds for comparative analysis. The mcr-1 gene was detected in a total of 12 isolates recovered from diseased production birds from China and Egypt. No mcr genes were detected in the healthy fecal isolates. The full mcr-1 gene from positive isolates was sequenced using specifically designed primers and were compared with sequences currently described in NCBI. mcr-1 positive isolates were also assessed for phenotypic colistin resistance and extended spectrum beta lactam phenotypes and genotypes. This study has identified mcr-1 in APEC isolates dating back to at least 2010 and suggests that animal husbandry practices could result in a potential source of resistance to the human food chain in countries where application of colistin in animal health is practiced.This article is published as Lima Barbieri, Nicolle, Daniel W. Nielsen, Yvonne Wannemuehler, Tia Cavender, Ashraf Hussein, Shi-gan Yan, Lisa K. Nolan, and Catherine M. Logue. "mcr-1 identified in avian pathogenic Escherichia coli (APEC)." PLoS One 12, no. 3 (2017): e0172997. DOI: 10.1371/journal.pone.0172997. Copyright 2017 Lima Barbieri et al. Attribution 4.0 International (CC BY 4.0). Posted with permission

Genetic Characterization of ExPEC-Like Virulence Plasmids among a Subset of NMEC

Neonatal Meningitis Escherichia coli (NMEC) is one of the most common causes of neonatal bacterial meningitis in the US and elsewhere resulting in mortality or neurologic deficits in survivors. Large plasmids have been shown experimentally to increase the virulence of NMEC in the rat model of neonatal meningitis. Here, 9 ExPEC-like plasmids were isolated from NMEC and sequenced to identify the core and accessory plasmid genes of ExPEC-like virulence plasmids in NMEC and create an expanded plasmid phylogeny. Results showed sequenced virulence plasmids carry a strongly conserved core of genes with predicted functions in five distinct categories including: virulence, metabolism, plasmid stability, mobile elements, and unknown genes. The major functions of virulence-associated and plasmid core genes serve to increase in vivo fitness by adding multiple iron uptake systems to the genetic repertoire to facilitate NMEC’s survival in the host’s low iron environment, and systems to enhance bacterial resistance to host innate immunity. Phylogenetic analysis based on these core plasmid genes showed that at least two lineages of ExPEC-like plasmids could be discerned. Further, virulence plasmids from Avian Pathogenic E. coli and NMEC plasmids could not be differentiated based solely on the genes of the core plasmid genome.This article is published as Nicholson, Bryon A., Aaron C. West, Paul Mangiamele, Nicolle Barbieri, Yvonne Wannemuehler, Lisa K. Nolan, Catherine M. Logue, and Ganwu Li. "Genetic characterization of ExPEC-like virulence plasmids among a subset of NMEC." PLoS One 11, no. 1 (2016): e0147757. DOI: 10.1371/journal.pone.0147757. Copyright 2016 Nicholson et al. Attribution 4.0 International (CC BY 4.0). Posted with permission